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Gao Y, Kim H, Kitata RB, Lin TT, Swensen AC, Shi T, Liu T. Multiplexed quantitative proteomics in prostate cancer biomarker development. Adv Cancer Res 2024; 161:31-69. [PMID: 39032952 DOI: 10.1016/bs.acr.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Prostate cancer (PCa) is the most common non-skin cancer among men in the United States. However, the widely used protein biomarker in PCa, prostate-specific antigen (PSA), while useful for initial detection, its use alone cannot detect aggressive PCa and can lead to overtreatment. This chapter provides an overview of PCa protein biomarker development. It reviews the state-of-the-art liquid chromatography-mass spectrometry-based proteomics technologies for PCa biomarker development, such as enhancing the detection sensitivity of low-abundance proteins through antibody-based or antibody-independent protein/peptide enrichment, enriching post-translational modifications such as glycosylation as well as information-rich extracellular vesicles, and increasing accuracy and throughput using advanced data acquisition methodologies. This chapter also summarizes recent PCa biomarker validation studies that applied those techniques in diverse specimen types, including cell lines, tissues, proximal fluids, urine, and blood, developing novel protein biomarkers for various clinical applications, including early detection and diagnosis, prognosis, and therapeutic intervention of PCa.
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Affiliation(s)
- Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hyeyoon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Gao Y, Wang YT, Chen Y, Wang H, Young D, Shi T, Song Y, Schepmoes AA, Kuo C, Fillmore TL, Qian WJ, Smith RD, Srivastava S, Kagan J, Dobi A, Sesterhenn IA, Rosner IL, Petrovics G, Rodland KD, Srivastava S, Cullen J, Liu T. Proteomic Tissue-Based Classifier for Early Prediction of Prostate Cancer Progression. Cancers (Basel) 2020; 12:cancers12051268. [PMID: 32429558 PMCID: PMC7281161 DOI: 10.3390/cancers12051268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 01/17/2023] Open
Abstract
Although ~40% of screen-detected prostate cancers (PCa) are indolent, advanced-stage PCa is a lethal disease with 5-year survival rates around 29%. Identification of biomarkers for early detection of aggressive disease is a key challenge. Starting with 52 candidate biomarkers, selected from existing PCa genomics datasets and known PCa driver genes, we used targeted mass spectrometry to quantify proteins that significantly differed in primary tumors from PCa patients treated with radical prostatectomy (RP) across three study outcomes: (i) metastasis ≥1-year post-RP, (ii) biochemical recurrence ≥1-year post-RP, and (iii) no progression after ≥10 years post-RP. Sixteen proteins that differed significantly in an initial set of 105 samples were evaluated in the entire cohort (n = 338). A five-protein classifier which combined FOLH1, KLK3, TGFB1, SPARC, and CAMKK2 with existing clinical and pathological standard of care variables demonstrated significant improvement in predicting distant metastasis, achieving an area under the receiver-operating characteristic curve of 0.92 (0.86, 0.99, p = 0.001) and a negative predictive value of 92% in the training/testing analysis. This classifier has the potential to stratify patients based on risk of aggressive, metastatic PCa that will require early intervention compared to low risk patients who could be managed through active surveillance.
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Affiliation(s)
- Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Yongmei Chen
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Hui Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Denise Young
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Yingjie Song
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Athena A. Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Claire Kuo
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Thomas L. Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA; (S.S.); (J.K.)
| | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA; (S.S.); (J.K.)
| | - Albert Dobi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | | | - Inger L. Rosner
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Gyorgy Petrovics
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, USA
- Correspondence: (K.D.R.); (J.C.); (T.L.)
| | - Shiv Srivastava
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
| | - Jennifer Cullen
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; (Y.C.); (D.Y.); (Y.S.); (C.K.); (A.D.); (G.P.)
- Center for Prostate Disease Research, John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (I.L.R.); (S.S.)
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (K.D.R.); (J.C.); (T.L.)
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.G.); (Y.-T.W.); (H.W.); (T.S.); (A.A.S.); (T.L.F.); (W.-J.Q.); (R.D.S.)
- Correspondence: (K.D.R.); (J.C.); (T.L.)
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Abstract
Multiple studies have confirmed that speckle-type pox virus and zinc finger (POZ) protein (SPOP) functions as a substrate adaptor of cullin 3-based E3 ligase and has a crucial role in various cellular processes via specific targeting of proteins for ubiquitination and subsequent proteasomal degradation. Dysregulation of SPOP-mediated proteolysis might be involved in the development and progression of human prostate and kidney cancers. In prostate cancer, SPOP seems to function as a tumour suppressor by targeting several proteins, including androgen receptor (AR), steroid receptor coactivator 3 (SRC3) and BRD4, for degradation, whereas it might function as an oncoprotein in kidney cancer, for example, by targeting phosphatase and tensin homologue (PTEN) for proteasomal degradation. In addition, nuclear SPOP targets AR for degradation and has a role as a tumour suppressor in prostate cancer; however, in kidney cancer, SPOP largely accumulates in the cytoplasm and fails to promote degradation of AR located in the nucleus, resulting in activation of AR-driven pathways and cancer progression. Owing to the context-dependent function of SPOP in human malignancies, further assessment of the molecular mechanisms involving SPOP in prostate and kidney cancers is needed to improve our understanding of its role in the development of these cancer types. Treatments that target SPOP might become therapeutic strategies in these malignancies in the future.
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Flores-Morales A, Iglesias-Gato D. Quantitative Mass Spectrometry-Based Proteomic Profiling for Precision Medicine in Prostate Cancer. Front Oncol 2017; 7:267. [PMID: 29164064 PMCID: PMC5674010 DOI: 10.3389/fonc.2017.00267] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/23/2017] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed cancer among men in the western societies. Many PCa patients bear tumors that will not threat their lives if left untreated or if treatment is delayed. Our inability for early identification of these patients has resulted in massive overtreatment. Therefore, there is a great need of finding biomarkers for patient stratification according to prognostic risk; as well as there is a need for novel targets that can allow the development of effective treatments for patients that progress to castration-resistant PCa. Most biomarkers in cancer are proteins, including the widely-used prostate-specific antigen (PSA). Recent developments in mass spectrometry allow the identification and quantification of thousands of proteins and posttranslational modifications from small amounts of biological material, including formalin-fixed paraffin-embedded tissues, and biological fluids. Novel diagnostic and prognostic biomarkers have been identified in tissue, blood, urine, and seminal plasma of PCa patients, and new insights in the ethology and progression of this disease have been achieved using this technology. In this review, we summarize these findings and discuss the potential of this technology to pave the way toward the clinical implementation of precision medicine in PCa.
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Affiliation(s)
- Amilcar Flores-Morales
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Diego Iglesias-Gato
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
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